Department of Bioengineering, Rice University, Houston, Texas 77005, USA.
J Chem Inf Model. 2012 Oct 22;52(10):2684-96. doi: 10.1021/ci300259u. Epub 2012 Sep 28.
Atom tracing provides valuable information in many analyses of metabolic networks including pathway inference and flux estimation. Symmetries-mapping operations that produce atom equivalencies-introduce alternative tracings when multiple atom mappings are aggregated. Although several attempts have been made to consider symmetry while curating atom mappings, a definition of the symmetry amenable to automated computation and a systematic quantification of the extent of symmetries in both compounds and reactions is still lacking. Moreover, the impact of symmetries on the calculation of the atom economy of pathways and the simulation of isotopomer distribution is yet to be assessed. In this study, we formulate the symmetries of both compounds and reactions as automorphic mappings of the corresponding graph representations. We investigate the extent of both compound and reaction symmetries in several metabolic systems. We find, through random walking in the metabolic network of E.coli , that alternative tracings originated from symmetries could give rise to considerable amount of differential conservation of atoms and distinct transition patterns of the isotopomer distribution.
原子追踪在代谢网络的许多分析中提供了有价值的信息，包括途径推断和通量估计。当聚合多个原子映射时，对称映射操作会产生原子等价物，从而引入替代的追踪。尽管已经有几次尝试在进行原子映射时考虑对称性，但缺乏适用于自动计算的对称性定义，以及化合物和反应中对称性程度的系统量化。此外，对称性对途径原子经济性的计算和同位素分布模拟的影响仍有待评估。在这项研究中，我们将化合物和反应的对称性表示为相应图表示的自同构映射。我们研究了几个代谢系统中化合物和反应对称性的程度。我们通过在大肠杆菌代谢网络中的随机游走发现，来自对称性的替代追踪可能会导致原子的大量差异守恒和同位素分布的不同跃迁模式。
